vartools-package: Variant Association tools

In izhbannikov/vartools: Variant Association Tools R-package

Description

vartools is an R-package for the analysis of rare variants and currently has the following methods: CMC, KBAC, RVE, VT, RareCover, RBT, C-alpha, etc.

Installation
git clone https://github.com/izhbannikov/vartools.git
R CMD INSTALL vartools

Details

Package:	vartools
Type:	Package
Version:	1.4.0
Date:	2015-10-04
License:	GPL (>= 2)
Project URL:	https://github.com/izhbannikov/vartools

Author(s)

Ilya Y. Zhbannikov

Maintainer: Ilya Y. Zhbannikov | [e-mail]

Examples

#CMC test
# Load the package
library(vartools)
?cmc

pgdata <- as.matrix(read.table(system.file("extdata","phengen.dat",package="vartools"), as.is=T, skip = 1))
cmc.test <- cmc(table=pgdata)
print(cmc.test)

#KBAC test
?kbac

alpha <- 0.05
num.permutation <- 3000
quiet <- 1
alternative <- 1
maf.upper.bound <- 0.05
casectrl.dat <- read.table(system.file("extdata","phengen.dat",package="vartools"), skip = 1) 
kbac.test <- kbac(table=casectrl.dat, alpha, num.permutation, quiet, maf.upper.bound, alternative)
print(kbac.test)

izhbannikov/vartools documentation built on May 18, 2019, 7:14 a.m.